well, i am not sure how difficult it would be for you to come back.  I am not sure if your sevis no is in the database of US embassy in Nepal.  I am positive about few things here:

you went back after your undergrad which shows that you were not interested in remaining in usa being illegal

you have very good GPA, which shows that you were good student

Also, you have a letter from human resources and says that it was a mistake. 

I believe these things should work in your favor.  do not talk about you being out of status until and unless you are asked to clarify.  have your transcript and GRE ready and apply.  Assistantship will always helps. good luck.